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- PDB-7l4s: Crystal structure of the OxyR regulatory domain of Shewanella one... -

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Basic information

Entry
Database: PDB / ID: 7l4s
TitleCrystal structure of the OxyR regulatory domain of Shewanella oneidensis MR-1, reduced form
ComponentsTranscriptional regulator of oxidative stress OxyR
KeywordsDNA BINDING PROTEIN / OxyR
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator of oxidative stress OxyR
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTao, Y.J. / Gao, H.
Funding support United States, China, 4items
OrganizationGrant numberCountry
Robert A. Welch FoundationC-1565 United States
Ministry of Science and Technology (MoST, China)2018YFA0901300 China
National Natural Science Foundation of China (NSFC)41976087 China
National Natural Science Foundation of China (NSFC)31930003 China
CitationJournal: Mbio / Year: 2022
Title: Functional Irreplaceability of Escherichia coli and Shewanella oneidensis OxyRs Is Critically Determined by Intrinsic Differences in Oligomerization.
Authors: Sun, W. / Fan, Y. / Wan, F. / Tao, Y.J. / Gao, H.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator of oxidative stress OxyR
B: Transcriptional regulator of oxidative stress OxyR
C: Transcriptional regulator of oxidative stress OxyR
D: Transcriptional regulator of oxidative stress OxyR
E: Transcriptional regulator of oxidative stress OxyR
F: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)202,8726
Polymers202,8726
Non-polymers00
Water6,071337
1
A: Transcriptional regulator of oxidative stress OxyR
C: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-11 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: Transcriptional regulator of oxidative stress OxyR
D: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-10 kcal/mol
Surface area17440 Å2
MethodPISA
3
E: Transcriptional regulator of oxidative stress OxyR

F: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_864-y+3,x-y+1,z-1/31
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.998, 83.998, 185.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Transcriptional regulator of oxidative stress OxyR


Mass: 33811.957 Da / Num. of mol.: 6 / Fragment: Regulatory domain / Mutation: C203S
Source method: isolated from a genetically manipulated source
Details: OxyR RD domain with C203S mutation and 6xHis tag at the N-terminus
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: oxyR, SO_1328 / Plasmid: pET-28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q8EHA1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.83 % / Description: Rod-shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drops were made by combining 1 ul of SoOxyR C203S RD with 1 ul of mother liquor containing 4.0 M ammonium acetate and 0.1 M Bis-Tris propane pH 7.0. Rod-shaped crystals appeared within 3 to 4 days.

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 57163 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.509 / Num. unique obs: 2815 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i69

1i69


Resolution: 2.4→42 Å / Cross valid method: FREE R-VALUE / σ(F): 182.18 / Phase error: 25.6731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 2830 4.96 %
Rwork0.1744 54280 -
obs0.1931 57110 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 0 337 9621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00549446
X-RAY DIFFRACTIONf_angle_d0.890112839
X-RAY DIFFRACTIONf_chiral_restr0.05291585
X-RAY DIFFRACTIONf_plane_restr0.00731612
X-RAY DIFFRACTIONf_dihedral_angle_d5.69351260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.31361360.25432691X-RAY DIFFRACTION94.92
2.44-2.490.30971420.24322708X-RAY DIFFRACTION95.02
2.49-2.530.31921520.23492713X-RAY DIFFRACTION94.69
2.53-2.580.29191720.22432675X-RAY DIFFRACTION93.96
2.58-2.640.27891520.2192710X-RAY DIFFRACTION94.69
2.64-2.70.23441170.2292781X-RAY DIFFRACTION95.9
2.7-2.770.3105900.20382724X-RAY DIFFRACTION96.8
2.77-2.840.25841340.2072713X-RAY DIFFRACTION95.29
2.84-2.930.28591500.20762705X-RAY DIFFRACTION94.75
2.93-3.020.28861360.20222728X-RAY DIFFRACTION95.25
3.02-3.130.23491480.19632744X-RAY DIFFRACTION94.88
3.13-3.260.27461320.18592735X-RAY DIFFRACTION95.4
3.26-3.40.24941650.19272658X-RAY DIFFRACTION94.16
3.4-3.580.19271100.18822751X-RAY DIFFRACTION96.09
3.58-3.810.23591680.17552704X-RAY DIFFRACTION94.15
3.81-4.10.19551600.17072671X-RAY DIFFRACTION94.18
4.1-4.510.19541650.16042701X-RAY DIFFRACTION94.18
4.51-5.160.1861400.14862725X-RAY DIFFRACTION95.11
5.17-6.50.24231610.18152704X-RAY DIFFRACTION94.38
6.51-420.2237980.20832741X-RAY DIFFRACTION95.84

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